Computer algebra system

Fermat — Computer algebra system that does arithmetic of arbitrarily long integers and fractions, multivariate polynomials, symbolic calculations, matrices over polynomial rings, graphics, and other numerical calculations.

FreeMat — Matlab-like program that supports many of its functions and features a codeless interface to external C, C++, and Fortran code, further parallel distributed algorithm development (via MPI), and 3D visualization capabilities.

Chemistry and biology

Computational biology and bioinformatics

BALL (Biochemical Algorithms Library) — Application framework in C++ that provides an extensive set of data structures as well as classes for molecular nechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

Quantum ESPRESSO — Integrated suite of applications for electronic-structure calculations and materials modeling at nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

Skychart / Cartes du Ciel — Planetarium that maps out and labels most of the constellations, planets, and objects you can see with a telescope. It can also download Digitized Sky Survey Charts and superimpose images over these charts.

KTechLab — IDE for electronic and PIC microcontroller circuit design and simulation featuring an extensive circuit designer with autorouting and simulation of all common electronic components and logic elements.